DNA Variations and Cell Molecular Stateome
DNA Variations and the Cell Molecular Stateome
DNA Variations Between Cells
DNA in cells within a single individual differs from cell to cell due to genomic and epigenomic variations.
Genome Differences:
- SNPs (Single Nucleotide Polymorphisms): These variations affect gene regulation.
- CNVs (Copy Number Variations): Variations in the number of copies of DNA sections.
- RIPs (Retrotransposon Insertion Polymorphisms): Most prominent in germ cells and some neurons.
- Insertions and Deletions: Other forms of genetic variation.
These variations contribute to distinct phenotypes. Humans share approximately 99.9% of the same DNA, and the remaining 0.1% accounts for phenotypic differences through variations in SNPs, RIPs, CNVs, and insertion/deletions. This principle also applies to cells, where these differences lead to normal, abnormal, or diseased states, meaning that no two cells have the *exact* same genotype.
Epigenome Differences:
The epigenome exhibits individual variation through:
- DNA Modification: Primarily methylation.
- Histone Modification: Including methylation, acetylation, and phosphorylation.
- Chromatin Modification: Open or closed states.
For example, a kidney cell differs from a neuron due to these genomic and epigenomic variations.
Identical Twins Study:
Researchers sequenced the genomes of identical twins (ages 3-74) and found that their genomes were not entirely identical. Epigenomic differences were more pronounced in twins raised apart and in older twins, highlighting the influence of environmental factors.
The conclusion is that no two cells have an identical genome, and no two individuals, not even identical twins, have the same phenotype.
The Cell Molecular Stateome (CMS)
The Cell Molecular Stateome (CMS) is a comprehensive framework that researchers use to characterize developing, normal, and diseased human cells across all 210 cell types.
Nuclear Analyses:
- Genome Sequencing: Next-Generation Sequencing (NGS) is used to sequence DNA and determine the genome.
- 4D Chromosome Analysis: Examination of chromosome territories, mRNA factories, and looping using FISH (Fluorescence In Situ Hybridization).
- Chromatin Analysis: Determining whether chromatin is open or closed (if a sequence is found, it is closed).
- Epigenome Analysis: Using ChIP (Chromatin Immunoprecipitation) to identify histone marks and bisulfite sequencing to identify DNA marks.
Cytoplasmic Analyses:
- Transcriptome: Identifying all mRNAs.
- Proteome: Identifying all proteins.
- Phosphoproteome: Analyzing proteins regulated by kinases (approximately 30% of proteins).
- Interactome: Studying protein-protein interactions.
Gene Regulation:
It is believed that 1-100 genes control cell type and whether a cell is normal or diseased. Knockdown experiments, using siRNAs (up to 90% knockdown) or CRISPR/Cas9, can determine the effect of these genes. To turn on a gene, researchers can use CRISPR/Cas9 or transfection. Only 2% of the human genome codes for exons, while 80-90% is involved in gene regulation at some point. Approximately 62% of the genome is transcribed into RNA, with 31% from exons and 31% from intergenic regions (where new genes can arise).